domesticated crop species. Rice is known to be a staple food for one third of the world s

Transcription

1 1 CHAPTER 1 INTRODUCTION Oryza sativa, commonly known as rice holds a unique position among domesticated crop species. Rice is known to be a staple food for one third of the world s population and also the first fully sequenced crop genome (Sasaki and Burr, 2000; Garris et al., 2005). Rice is known as model crop due to its diploid genetics (2n=24), relatively small genome size (Kurata et al., 1994; Xu et al., 2005), significant level of polymorphism (McCouch et al., 1997), large amount of well conserved genetically diverse material and its adaptations to wide range of geographical, ecological and climatic regions. The cultivation and selection of rice by farmers and researchers under varied environmental conditions resulted in the development of abundant rice cultivars. It has been reported that ~120,000 distinct rice varieties exist in the world, which are grown in more than 100 countries (Singh, 2011). Thus, rice cultivars offered extensive opportunities to researchers for employing different characterization approaches in order to study the varietal divergence among them. Among all the Asian countries, India is blessed with a great diversity of rice germplasm in its vast territorial land area accounting for about 20% of all world rice production (Parikh, 2012). The cultivars have been developed through selections, based on desirable characters (grain yield, aroma, grain length, cooking quality) and adaptation to environmental stresses (Pachauri et al., 2013). Aromatic rice cultivars constitute a small but special group of Indian rice cultivars and are considered best in terms of quality and aroma (Singh et al., 2000).

2 2 Among aromatic rice cultivars, basmati rice of Indian sub-continent clinched a premium status. Basmati rice cultivars are characterized by extra long superfine slender grains and pleasant aroma after cooking (Bhattacharjee et al., 2002). In India, basmati rice cultivars are cultivated mainly in the foothills of the Himalayas, Haryana, Punjab and Uttar Pradesh regions of India (Nagaraju et al., 2002). India produces about 70% of the world s basmati production and nearly two third of the total production is exported to other countries (Verma et al., 2012). With growing demand for aromatic rice in the local and international market, high emphasis has been laid on development and improvement of basmati types. In spite of high quality traditional basmati varieties in India, the research is continued for the development of many new basmati and hybrid varieties of rice with better quality and agronomic traits to meet the consumer and farmers demand (Joshi and Behera, 2006). Systematic study and characterization of high quality rice germplasm is not only important for utilizing the useful donor traits, but also essential in the present era for protecting the unique rice varieties. Characterization is a critical step to find genetic relationships among genotypes and to prevent adulteration practices. The study of genetic relationship among different rice cultivars is considered to be an important tool for plant breeders for an efficient selection of the diverse parents for their potential use in a rice breeding program as well as for the improvement of quality traits of rice (Sajib et al., 2012). Moreover, characterization is also essential to prevent adulteration of low priced, non-aromatic rice with high priced aromatic rice and consequently dissemination of information to the consumers. Unambiguous, reliable, fast and cost-effective identification of genetic divergence in rice cultivars is essential for the effective utilization and protection of plant genetic resources (Paterson et al., 1991; Barcaccia, 2009). According to International Union for Protection of New Plant Varieties (UPOV),

3 3 any new characteristics used in varietal characterization should be clearly defined, accepted and should have standard method of observation, least or not affected by environment, accessible to breeders, associated with reasonable costs and efforts. Different approaches based on morphological, physico-chemical, biochemical and molecular attributes have been used to achieve characterization of genetic divergence among rice cultivars (Chakravarthi and Naravaneni, 2006). The quality of rice grain assumes greater importance, because most of the rice produced is cooked and consumed as a whole kernel, whereas the percentage of rice converted into flour or flakes being very small (Huang et al.,1998). The genetic diversity among rice cultivars from quality point of view can be assessed in three broad categories, i.e. physical, processing and nutritional qualities (Thongbam et al., 2011). The shape and size of grain, chalkiness and alkali spreading values are considered under physical qualities. Milling, cooking, textural and thermal attributes are considered as processing qualities, which are in turn greatly influenced by amylose content (Webb, 1980; Juliano, 1985), gel consistency (Cagampang et al., 1973) and gelatinization temperature (Little et al., 1985). The nutritional qualities of different rice grains depend upon protein, carbohydrate, starch, ash, fat, minerals, vitamins and amino acids content. Data related to the characteristics of basmati and non-basmati rice grains is useful for preparation of novel rice based food products satisfying consumer requirement. Therefore, the characterization of morphological, physico-chemical, cooking, eating, and textural properties of rice grains determine the overall assessment of divergence among rice cultivars based on quality traits (Yadav et al., 2007). Though physico-chemical characterization seems to be useful for determining the genetic divergence among rice cultivars but some varieties with different qualitative properties are morphological indistinguishable. Moreover, genetic diversity among

4 4 different morphological and phenological attributes varies with environment and evaluation of these traits requires growing the plant to full maturity prior to identification (Chakravarthi and Naravaneni, 2006). To overcome the limitations, many DNA marker based approaches have been developed for characterizing the rice cultivars; which offers additional advantage of screening at early stage with simplicity and accuracy. Molecular markers proved to be effective in finding out uniformity, distinctness and stability in different rice cultivars (Sarao et al., 2010). DNA based markers are neutral having no phenotypic and epistatic effect (Ye-yun et al., 2005). Molecular markers are also useful in food traceability at any stage of food chain to certify the origin and quality of product to prevent the fraudulent approaches (Cirillo et al., 2009). The main DNA markers used for diversity assessment of rice cultivars are Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers (Rana et al., 1999; Lu et al., 2002; Saini et al., 2004). SSR markers have much more polymorphism than most of the other DNA markers as they are co-dominant in nature and are available in large quantity (Ye-yun et al., 2005). They are abundant, hypervariable, multiallelic and evenly distributed throughout the nuclear genome and provide a valuable source of polymorphism, making them important class of genetic markers (Varshney et al., 2005). Due to polymorphic nature, many SSR markers are considered undisputed when analyzing closely related varieties (McCouch et al., 2002). Therefore, SSR has become the most popular and ideal marker in identification of plant variety like rice on basis of DNA fingerprinting technique (Nagaraju et al., 2002; Singh et al., 2004; Sarao et al., 2010).

5 5 New varieties may not always significantly different from the existing varieties in some quality attributes and therefore, it is very crucial to monitor the quality parameters of new varieties that are in the pipe line. Studies on characterization of quality attributes of developed and under development rice cultivars are mandatory for the improvement in rice quality and to meet the increasingly alternative demands of consumers everywhere. The main concern of consumer is to get high quality rice varieties, which in turn largely depends on physicochemical and cooking properties of milled rice grains (Bhattacharjee et al., 2002). However, the introduction of new rice varieties into the germplasm, necessitating the assessment of their molecular diversity before an elimination of the redundant rice genotypes. Different types of data sets based on morphological, physico-chemical and molecular characterization have been usually used to assess genetic diversity among different types of rice accessions. The multivariate methods have been further used to cluster the rice accessions into groups by taking into consideration the relationship among characterized attributes. The use of different statistical techniques for analysis of multivariate data can help to identify the group of genotypes with similar characteristics in a more significant manner. Rice cultivars identified on the basis of multivariate analysis divergence would be more promising for any breeding and rice product development program as compared to particular single type of characterization (Arunachalam, 1981; Gouvea et al., 2010). Further, the efficient discriminative safeguards are required to detect the adulteration and to protect the quality of the export consignments of basmati (Singh et al., 2011). There are very few reports available to show the comparison among different methods to estimate the genetic diversity among basmati and non-basmati rice cultivars. Though, characterization of different rice cultivars by multivariate approaches is mandatory for the effective rice breeding and quality improvement, yet it is highly

6 6 essential that these valuable parameters are to be collected, conserved, and properly documented in database to get a quick access about different parameters of any particular cultivar of rice at any time (Ramalingam et al., 2010). Presently, information regarding physico-chemical and molecular analysis of rice germplasm is rarely documented in the form of a well structured database. The development of such database would help in the development of specific rice food products having desired quality attributes, detects adulteration and also estimate genetic divergence among basmati and non-basmati rice cultivars. Keeping in view of the above, the present study has been undertaken to fulfill the following objectives: 1. Physico-chemical characterization of Indigenous basmati and non-basmati varieties of rice. 2. Molecular characterization of basmati and non-basmati varieties of rice. 3. Detection of adulteration in rice by using molecular markers. 4. Comparative analysis of physico-chemical and molecular characterization for detection of adulteration. 5. Designing of database on basis of physico-chemical and molecular methods using bioinformatics and statistical tools.